PF3D7_1404000 (RPB4)

Genome location: Pf3D7_14_v3:143,936..144,696(+)

Genome classification: Core

Function and Localization

Product Description: DNA-directed RNA polymerase II subunit RPB4, putative

SignalP Peptide: N/A

# Transmembrane Domains: 0

EC Numbers: 2.7.7.6 (DNA-directed RNA polymerase)

Curated GO (PlasmoDB): None

Expression by stage (LR - Le Roch et al., and MCA - Malaria Cell Atlas):

Stage	LR class	MCA mean	MCA prop. zeros
Sporozoite	not expressed	N/A	N/A
Ring	not expressed	0.05	0.98
Trophozoite	possibly expressed	0.23	0.85
Schizont	possibly expressed	0.08	0.94
Gametocyte	expressed	0.40	0.77

More info:

Resistome Mutations

Old (Pf3D7v3) Gene ID: PF3D7_1404000

Resistome Missense Mutations: None

Resistome Compounds with Missense Mutations: None

Resistome # Samples with Disruptive Mutations: 0 (0 missense, 0 "interesting" missense)

Essentiality (ABS)

Zhang Phenotype: Non - Mutable in CDS *tentative

MIS: 0.361 | MFS: -2.59 | #Insertions: 0

PlasmoGEM Phenotype: Essential (Pb ortholog: PBANKA_1038100)

Relative Growth Rate: 0.33 ± 0.26
Confidence: 4.10

RMgmDB ABS Phenotype: N/A

More info: PhenoPlasm Link

Binding Evidence

AlphaFill Uniprot ID: Q8IM54

"Best" AlphaFill ligand hit: No AlphaFill hits

BRENDA EC Inhibitors:

EC #	Name	EC Inhibitors
2.7.7.6	DNA-directed RNA polymerase	BRENDA SOAP query unsuccessful

No evidence of orthology to BindingDB entries

Orthology Information

Ortholog Group (OrthoMCL): OG6_532998

No human ortholog(s)

Genetic Variation

MalariaGEN Pf7 (worldwide samples) # unique SNV/indels:

Homozygous genotype calls only

variant type	common	rare	doubleton	singleton
synonymous	4	1	6	8
disruptive	0	9	9	19
missense	0	8	9	18

Any inclusion in genotype call

variant type	common	rare	doubleton	singleton
synonymous	4	11	6	7
disruptive	1	34	19	32
missense	1	25	17	19

PlasmoDB Total SNPs: 20

Non-coding: 12 | Synonymous: 7 | Nonsynonymous: 0 | Stop Codon: 1

Protein Information

Protein Length: 165 | Molecular Weight (kDa): 20.05

UniProt ID(s): Q8IM54

PDB ID(s): None

Isoelectric Point: 7.39

Protein Domain Annotations:

Source	Family ID	Description
InterPro	IPR005574	RNA polymerase subunit RPB4/RPC9
InterPro	IPR010997	HRDC-like superfamily
PFam	PF03874	RNA polymerase subunit RPB4/RPC9
Superfamily	SSF47819	HRDC-like superfamily

Associated Publications

PMID	Title	Authors	DOI/Link
12368864	Genome sequence of the human malaria parasite Plasmodium falciparum.	Gardner MJ, Hall N, ..., Barrell B	10.1038/nature01097
32518159	The yeast exoribonuclease Xrn1 and associated factors modulate RNA polymerase IIprocessivity in 5' and 3' gene regions	Fischer J, Song YS, ..., Choder M	10.1074/jbc.RA120.013426
33094674	Rpb4 and Puf3 imprint and post-transcriptionally control the stability of acommon set of mRNAs in yeast	Garrido-Godino AI, Gupta I, ..., Navarro F	10.1080/15476286.2020.1839229
35216121	The Association of Rpb4 with RNA Polymerase II Depends on CTD Ser5P PhosphataseRtr1 and Influences mRNA Decay in Saccharomyces cerevisiae	Garrido-Godino AI, Cuevas-Bermudez A, ..., Navarro F	10.3390/ijms23042002
35905859	Rpb4/7, a key element of RNA pol II to coordinate mRNA synthesis in the nucleuswith cytoplasmic functions in Saccharomyces cerevisiae	Garrido-Godino AI, Martin-Exposito M, ..., Navarro F	10.1016/j.bbagrm.2022.194846
35051353	Structural visualization of de novo transcription initiation by Saccharomycescerevisiae RNA polymerase II	Yang C, Fujiwara R, ..., Murakami K	10.1016/j.molcel.2021.12.020